ATOM : setup blender python environment in my IDE
First of all you'll need to make sure, that Atom knows how to lint and autocomplete python-code (there should be plenty of packages to achieve that). 

Test your auto-completion and package access with common packages (e.g. os). Make sure it works as desired.

If so, the only thing left to do is to get Blender into your python environment. You can either 


compile Blender as a python package yourself and add it to the site-packages folder of your python installation
or use pip to install the bpy package, that should add Blender as a precompiled module (I don't know, how well it's been maintained though).